The present study evaluated the antifungal activity of honey samples collected from different locations at Khyber Pakhtunkhwa (KPK, Pakistan). Disc diffusion method was used to test the antifungal potential of twenty-one (branded, unbranded, and natural comb) honey samples from the different botanical origins at different concentrations (undiluted, 10%, 30%, and 50%, w/v) against Candida albicans and Rhodotorula species. Branded, unbranded, and natural comb honey samples generate different inhibition zones (4-13 mm, 5-15 mm, and 8-17 mm) against Rhodotorula species. Candida albicans showed resistance for all tested honey samples. Minimum inhibitory concentration (MIC) against Candida albicans and Rhodotorula species were 53.33%-88.12% and 1.76%-90.22% for branded, 61.3% – 93.8% and 9.90% – 95.5% for unbranded, and 67.1%-96.8% and 6.39%-98.8% for natural comb honey. In conclusion, natural comb honey from Khyber Pakhtunkhwa may have antifungal therapeutic potential and could be a useful source for generating functional food.